For my work I needed to merge differences between two files into a new file and doing this by just watching output from 'diff' is a little bit too annoying to do. I remembered somebody recommending Meld too me. It shows the differences in a clear graphical way and also allows you to edit the text in the files, which is ideal for a scripting language like PHP. It saved me a lot of problems merging the changes, the only 'problem' is that it doesn't integrate with Subversion the version control system we use for eZ Publish.
Here is also a screenshot of Meld in action: